


Molly's Secret

by Minirose96



Category: Sherlock (TV), Sherlock Holmes & Related Fandoms
Genre: And liked it?, Blow Job, Carpet Sex, F/M, Possible Dub-Con, Rug Burn, Sex, What if - Molly knew about Jim's real self, molliarty - Freeform
Language: English
Status: Completed
Published: 2014-11-29
Updated: 2014-11-29
Packaged: 2018-02-27 09:27:23
Rating: Explicit
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,827
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2687675
Author URL: https://archiveofourown.org/users/Minirose96/pseuds/Minirose96
Summary: <blockquote class="userstuff">
              <p>"Molly was surprised when she discovered Jim from IT's true nature. Surprised, but not necessarily repulsed."</p><p>This was actually written LAST Christmas, for the Sherlockmas fan art exchange. It was written for Apple_Pathways on livejournal, who showed some interest in Molliarty, and at the time I was still kind of jumping from ship to ship, and I loved the idea of sweet Molly Hooper dating Jim, even knowing his past. </p><p>So, this story is somewhat canon-aligned, going from approximately the lab scene where Sherlock tells Molly Jim's gay to The Locker Room scene from the previews.</p>
            </blockquote>





	Molly's Secret

**Author's Note:**

  * For [Apple_Pathways](https://archiveofourown.org/gifts?recipient=Apple_Pathways).



When Sherlock Holmes blurted out that Molly's new boyfriend Jim was gay, she didn't hold much stock in it. She was insulted for Jim when she ran out of the room. It always had to be him, to spoil the one thing that had started to make her happy. Jim made her very happy. He made her feel beautiful, and cherished. She felt safe with him. And he most certainly was not gay, if the activities of the night before had anything at all to say about that.

She ignored Sherlock, in the end. He was the one who constantly treated her poorly, like an assistant or intern rather than the skilled pathologist she was. He only wanted her for her job. If it wasn't for that, she'd be useless to him.

Jim on the other hand, liked her for being herself. She could talk about her job, and he was oddly accepting of when she went into a little too much detail about the cadavers she worked on. He was wonderful, and so accepting of her job. And he didn't mind curling on the couch with her and Toby, and watching Glee when she was in the mood for a cuddle. That was always good. He was good. Sherlock could piss off if he wanted to ruin it.

When Molly found out that 'Jim from IT' was actually James Moriarty, the man who'd been strapping bombs to people, she was astonished, shocked, and a bit scared. She was also fascinated. For her, Fascination won out, every time.

When he came over the next day, Molly smiled, and let him in just like every other day. They sat together and watched Glee. He was sitting up on the couch, but she was laying down, her head in his lap,and he was absentmindedly running his fingers through her hair as she explained the day's cadavers and the newest case Sherlock was working on, though she didn't have many details yet.

When she asked him about it plainly, he had been more than happy to fill her in, and she had listened attentively.

One thing she was certain of was that Jimmy was a genius, up to and perhaps beyond Sherlock's levels. She also knew he wasn't a very nice man by most peoples' standards. After all, strapping bombs to innocent people wasn't very nice. But he was nice to her. He made her feel special, that she had somehow caught the attention of the world's only consulting criminal, and kept it.

So, their routine changed a bit. He couldn't come over as often, seeing as he had a huge criminal kingdom to rule over, but they arranged meetings, dates, and he still managed to come over at least once a week, to remind her how much he loved his mousy little Molly. They say together on the couch, exchange how their day went, she'd make dinner, and he'd stay the night if he could.

He never hid anything from her. She heard who he had killed, what his plans for his game with Sherlock were, and how he intended to get what he wanted. She loved his honesty. It was more than most people had ever offered her. She never helped with anything, though, and told him that she would never alter evidence to save him if it came to that.

He'd simply chuckled, and told her she'd never get anything he didn't want her to get. And she believed him.

It worked out like that for a long time, several months in fact.

Then, just after the case that made Sherlock famous, the Reichenbach case, Jim just stopped coming over. When she tried texting the secure line he'd given her, the number was cancelled. She should have known something like this would happen, but she had let herself get comfortable.

Then, not two weeks later, she hears that Jim was arrested for attempting to steal the crown jewels, while also having orchestrated the unlocking of the cells at Pentonville Prison, and opening all the vaults in the Bank of England. It just didn't seem right. Jim wouldn't let himself be caught like that.

But he hadn't told her anything. It was another of his plans, and she'd been left unawares of this one. Oh, she knew it had something to do with Sherlock. That much was obvious. She just can't figure out his plan. Of course not, she'd no genius. She's just ordinary Molly Hooper, the girl always forgotten, and never cared about.

It came as no surprise to her when Jim was acquitted. She knew his style, he's probably threatened the jurors. Still, so obvious. She wanted desperately to know what he was playing at.

… … … … … …

She'd finally begun to lose her silly crush on Sherlock when Jim began to love her. Or, she thought he had. Now, the sad look on Sherlock's face made her realize just how vulnerable, how human, he was. He could be so mean sometimes, but he was a good man, in the end. He cared about his friends, about those people who mattered – unlike her – and he didn't deserve to look so downtrodden because of what was going on.

It was, in the end, the lingering bits of her crush on him that made her want to comfort him. And she'd always done what he wanted, even when she was with Jim. Now, she wanted to do more. It was a bit silly really, but she felt this would make a bit of amends for all the times she'd held back information that might have saved someone's life, simply because she'd fallen in love with a psychopath.

Was still in love with him, really, but that didn't matter. He'd left her alone, so it was her job to pick up the pieces – again – and restart – again. And helping Sherlock now, when he was at his worst, seemed a good way to do so.

"You're a bit like my dad. He's dead – No sorry!" She winced. This wasn't working.

"Molly, please don't feel the need to make conversation it's really not your area." His tone was almost condescending. Still, she couldn't give up.

"When he was dying he was always cheery. He was lovely, except when he thought no one could see… I saw him once. He looked sad."

"Molly." He said in a warning tone.

"You look sad, when you think he can't see you."

Finally, Sherlock raised his eyes from the microscope.

"Are you okay? And don't just say you are, because I know what that means, looking sad when you think no one can see you."

"You can see me."

"I don't count." She said, glancing away for a moment before looking back up at him. "What I'm trying to say is, if there's anything I can do, anything you need, anything at all, you can have me." Wait, not, wrong wording, umm… "No, I just mean… I mean, if there's anything you need… it's fine."

"But what could I need from you?" His voice wasn't condescending anymore. He was looking at her weirdly. She had to glance away again.

"Nothing… I dunno. Probably say thank you, actually."

"Thank you?" It sounded more like a question than actual thanks.

She couldn't stand it anymore. She had to get out. "I'm just going to get crisps, do you want anything? It's okay, I know you don't." she said, stepping around him and heading for the door.

"Well actually I –"

"I know you don't." She interrupted, before almost scurrying out the door. So embarrassing.

By the time she got back, both of them were gone. She figured that was the end of it, all of it. Sherlock would go back to normal. She'd still be alone. Everything back to how it was before.

How wrong she was.

… … … … …

Later that day, while she was sitting on her couch, reading one of her texts with Toby curled up beside her, she heard her front door open. Only, she hadn't invited anyone over, and the door had been locked anyway.

She looked up as a familiar face came in. For the first time, she was a bit scared.

It was Jim. And he looked angry.

"Did you miss me, little mouse?" Jim asked, walking into her living room. His arms were folding neatly behind his back as he stalked towards her.

Molly gulped slightly, and quickly set her book aside as she sat up straight on the couch. She looked slightly down. "W-what are you doing back here? You haven't. . . come around in weeks."

Jim chuckled, stepping closer. "Did you really think I'd leave, little mouse?" He asked, though it wasn't really a question. "I told you before, you're mine, and I don't leave my things unattended forever. But now, you've been a naughty little mouse, haven't you?"

Molly quivered softly, watching Jim with wide eyes as she wavered on the edge of getting up and running away from him, or running towards him. "You left. I didn't think you'd come back, since I'm not as interesting as other...things. But… I don't know what you mean. I haven't done anything." She knew it might be a risk, arguing against him about whatever she'd done wrong, but she hadn't done  _anything._

"That's where you're wrong, little mouse." Jim said, continuing his slow pace closer. "I find you  _very_ interesting. Especially after that stunt you pulled, comforting Sherlock, pulling him from the rut I've dug for him." he tutted like a parent would to a child.

Molly frowned, realizing at least what she'd supposedly done wrong. "He needed someone to help him. I've told you before Jim, I would never do anything to hurt anyone. He was hurting." She stayed as still and stiff as she could, not wavering in her resolve, even if Jim was stalking her like prey.

Finally, he came to a stop in front of her, and lifted her head up with a hand on her jaw none-too-gently. He tutted her once more, smirking. "You mistake me." He scolded meeting her eyes as his other hand gripped both her wrists, and held them together in her lap. "I'm proud of you, little mouse. You've kept my main entertainment interesting. Now I can continue our game with some real opposition."

Molly pressed herself against the back of the couch, only just managing not to flinch away from Jim's touch. She tugged lightly against the grip on her wrists, staring into Jim's dark, chilling eyes. "You're...pleased?"

Jim smiled darkly, his grip loosening to release her wrists. "Very, little mouse. I had hoped something would give him a little push back to his usual self again. It's too fun to play with a beaten opponent." His eyes darkened once more. "But if you ever truly turn from me, I will burn you, just as I will burn him once our game is really over."

She shook her head solemnly, hesitating for a moment before she shifted forward, lightly pressing against Jim. She wrapped her now-free around him as she replied. "You know I wouldn't do that."

Jim smirked. "Good. I'd hate to put down my favorite pet." he said, his tone lightening slightly. "Just keep playing the hopeless pathologist for him."

Molly frowned slightly. It never was some show. She really was hopeless for him. He was brilliant, even with Jim with her, making sure she knew who she belonged to now. "All right." She muttered softly. "Is that the only reason you came back?"

Jim smirked, and bent forward to whisper in her ear. "Why, do you want to play, little mouse?" he placed his hands on either side of her head on the back of the couch, keeping her there.

Molly shivered, raising her gaze to meet his. There it was, the fire in her belly he brought, now that he was no longer trying to scare her. "You have been gone for an awfully long time," she murmured, looking through her lashes as she brought her hands back to trace along his chest.

"Yes, I have." She could hear the smirk in Jim's tone as he nipped at her neck. Molly let out a heavy breath, barely less than a sigh, as she curled her fingers in his shirt and tilted her head to the side to give him more access.

"Have you missed me?" He asked, purring into the skin on her neck before kissing a path from the hollow behind her ear, to her lips. He hovered over, waiting for her response.

"God, yes." She said, leaning forward to close the space.

Their lips melded together, and Molly's parted eagerly under his. He tasted her thoroughly, exploring every inch of her mouth with his tongue. Her sweet, decadent little mouth.

Suddenly, Jim pushed her off the couch onto the ground. She let out a little squeak of protest, but it faded as she saw what he was doing, yanking down his trousers and pants before taking the seat she'd just occupied.

His cock was hard and erect between his legs. She licked her lips as she glanced from it to his eyes, dark and lustful.

Jim raised his brow, the look he gave her somewhere between a dare for her to act, and a warning that if she didn't, he would.

Molly was more than happy to step up to the challenge. She sat up on her knees between his legs, and slowly drew her tongue up his shaft, licking a path to his head.

Jim kept his face blank, simply leaning against the back of the couch, but Molly could tell by the slight twitching of his fingers on his knees that he was pleased with her beginnings.

She smirked playfully, and ran her tongue across the head again before she wrapped her lips around him, and sucked lightly. He couldn't hold in the soft growling sound he made in the back of his throat.

The sound spurred her on. She ran her tongue along the bottom of his shaft as she took more of him into her mouth. She hollowed her cheeks, sucking just like he liked her to.

Suddenly, he stood and pushed her away, a feral look in his eyes.

"Wha –" She didn't get a chance to finish her question before he was pushing her down onto the carpet, and tugging away at her pants. He yanked them off of her, her knickers going as well, and without any preparation or preamble, He was on top of her, and shoving into her.

It burned slightly, but she was wet enough that it wasn't long before the slide of him in and out of her felt amazing.

She mewled under him, and clawed at the fabric of his shirt as he thrust into her. It felt so dirty, doing this while they were both still half-dressed, but it was too good to stop just to expose more skin.  
She tugged him down, and kissed his hungrily, loving the animalistic growls he made.

He wasn't gentle in the least with her. He bit her bottom lip hard as they kissed, and she let out little mewls as he squeezed her breasts through her shirt, the fabric rubbing against her erect nipples almost to the point of pain.

He came with grunt, shoving into her as she wrapped her legs around his waist to keep him from moving immediately away from her.

He ran her hands lightly through his hair, lightly motions as he came down from his sexual high. It didn't matter that she hadn't come too. It was always about making Jim happy, and if the light kisses he was giving her on her neck were anything to go by, he was very happy with her right now.

Molly was almost disappointed when he slid out of her, and forced her legs off of him before standing, and immediately grabbing his pants and trousers from the ground. He pulled them both on, and looked down at her until she sat up.

She crossed her legs in front of her, and tugged down the hem of her shirt to partially cover herself. She would have loved to have stayed there a bit longer, and cuddle. Now, she could feel where the carpet had burned her arse from the force of their rocking as he had shoved into her.

"Get dressed, Molly. There's no reason to sit there like a lump." He said, sitting down again on the couch. If not for the slight build of sweat on his forehead, you'd never have been able to tell he'd just had sex with her.

She sighed softly, and stood, grabbing her clothes and heading towards the bathroom. Unlike certain people, she had to clean up a bit before she could just shuck on her clothes. She went to the bathroom, and used a clean wash cloth to wipe away the sweat and cum residue between her legs before tossing it into the hamper.  
She pulled on her knickers and trousers, and made sure she at least looked a bit more presentable before going back out into the living room.

By then, Jim was gone. There was just a note on the table.

_I'm sorry little mouse, but I got an important call. Apparently, our favorite consulting detective has finally figured out a big part of my plan, so I've got to sort a few things out._

_Don't worry, I'll be back for you. Daddy would never leave his favorite toy alone for too long. I'll be back by the end of the week, when Sherlock and I have finished out game. I look forward to seeing you again, my dear._

_You know, mouse may be too soft of a term. Maybe when I get back, I'll let you know what animal I think matches you better._

_~ JM_

Molly reread the note several times, unable to believe what was on the small page, torn from one of her own notebooks. Well, she could believe it, but she hadn't thought until then Jim would have the audacity to actually leave right after they'd just had sex.

It was rude, and made her feel used, even more-so than when Sherlock used compliments to get what he wanted from her. She glared at the note for several minutes, before she crumpled it up, and threw it into a trash bin on the way back to the bathroom.

Suddenly, she felt the need for a shower. She wanted to remove every trace of that bastard from her skin.

… … … … … … …

It was a couple days later, with Jim's actions still fading in and out of her mind, she saw Sherlock as she was leaving the morgue.

"You're wrong you know." She turned sharply to as she spoke, her eyes wide and her hand over her heart. He'd given her a fright, until she realized it was him. And he kept talking, talking and advancing.  
"You do count. You've always counted and I've always trusted you. But you were right. . . I'm not okay."

"Tell me what's wrong." She asked nervously, worrying her bottom lip with her teeth.

"Molly, I think I'm going to die." His voice sounded almost dead to her ears. She had to help him, like she promised she would.

"What do you need?" she asked immediately. She knew, in the back of her mind, Jim wouldn't like this. Right now, she didn't care. It served him right, her helping Sherlock, after the way he'd treated her.

"If I wasn't everything you think I am, everything I, think I am, would you still want to help me?"

"What do you need?" she repeated, unwavering. She'd help him. She'd always help him.

"You." He said, coming to a stop in front of her. If she thought her heart was beating fast before, it was nothing to the pounding in her chest now.

Before she could speak though, he continued. "I need your help, to fake my death."

He filled her in on the plan, and there was nothing she could do but nod, and accept everything he said, and do everything he asked.

She watched from the window as he plummeted. She winced as he hit the ground. It was such a risky plan. She just prayed it worked.

The paramedics came, and it was time for her to get into her place, in the morgue. Now was the moment of truth. Either he was dead, or it worked.

… … … … … …

It worked. He washed him off of the blood as he slept in an almost coma like state, and in thirty minutes time, he was awake. He thanked her, and, in a move that seemed to surprised them both, pulled her against him, in a warm hug before leaving without another word. It left her more than a little confused. She had no clue what to do, except to go home. So she did.

She went home with a soft sigh, and snuggled into her bed with her cat, hoping that maybe the next day would be better.

… … … … … … …

She turned on the telly, and watched the news, waiting to hear what they had to say.  
Not much she hadn't expected, honestly. Just more useless dribble about how Sherlock was a fake, dead, committed suicide at St. Bart's.

And… the body of Richard Moran on the roof, where Sherlock and Jim had met. A single bullet wound through his skull, self-inflicted. That was a bit new. She wondered what had happened. She hadn't been told about much of anything.

Then her mind flicked to Jim. That name was linked to him, she knew. What had it been about? What if… What if… She swallowed. No, there was no what if's. She remembered where she'd heard that name. It was in the newspapers, in the article released by Kitty Riley. It was Jim. Of course it was. He'd killed himself, all for his stupid game with Sherlock. A game he'd lost.

She should have known he'd never come back for her. This was probably all part of the plan. He'd just used her, like everyone else.

It seemed her curse, to love men who would never stay with her.

She pulled the couch cover over her shoulders, and finally cried, for everything. For the time spent and lost with Jim. For the time Sherlock had used her. For all the time wasted. She just cried.

… … … … … … … … …

Two years after everything happened, Molly was better. Not the same, but better.

She was in the locker room at Bart's, putting her things away as she prepared to check out. Through the mirror of her locker, she saw a familiar figure, lean, exhausted, and a little worse for the wear, but familiar none the less.

She turned on her heel, and stared at the familiar face.

His lip quirked up into the barest hint of a smirk.

"I'm back, Molly."

She smiled just slightly. "I always knew you would be, Sherlock."


End file.
